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Series GSE101581 Query DataSets for GSE101581
Status Public on Mar 16, 2018
Title The cis-regulatory dynamics of embryonic development at single cell resolution
Organism Drosophila melanogaster
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Single cell measurements of gene expression are providing new insights into lineage commitment, yet the regulatory changes underlying individual cell trajectories remain elusive. Here, we profiled chromatin accessibility in over 20,000 single nuclei across multiple stages of Drosophila embryogenesis. Our data reveal heterogeneity in the regulatory landscape prior to gastrulation that reflects anatomical position, a feature that aligns with future cell fate. During mid embryogenesis, tissue granularity emerges such that cell types can be inferred by their chromatin accessibility, while maintaining a signature of their germ layer of origin. We identify over 30,000 distal elements with tissue-specific accessibility. Using transgenic embryos, we tested the germ layer specificity of a subset of predicted enhancers, achieving near-perfect accuracy. Overall, these data demonstrate the power of shotgun single cell profiling of embryos to resolve dynamic changes in open chromatin during development, and to uncover the cis-regulatory programs of germ layers and cell types.
 
Overall design sci-ATAC-seq data was collected on whole Drosophila embryos collected from 3 time points - 2 to 4 hours after egg laying (AEL), 6 to 8 hours AEL, and 10 to 12 hours AEL). In total, we collected data on 23,086 individual cells. Custom scripts for processing data are available at https://github.com/shendurelab/fly-atac. This series includes bulk DNAse-seq samples from wildtype, elav+, or Mef2+ 6-8 hr embryonic nuclei.
 
Contributor(s) Cusanovich DA, Reddington JP, Garfield DA, Daza RM, Aghamirzaie D, Marco-Ferreres R, Pliner HA, Christiansen L, Qiu X, Steemers FJ, Trapnell C, Shendure J, Furlong EE
Citation(s) 29539636
Submission date Jul 18, 2017
Last update date May 15, 2019
Contact name Darren A. Cusanovich
E-mail cusanovi@uw.edu
Organization name University of Washington
Department Genome Sciences
Street address Foege Building S-250, Box 355065, 3720 15th Ave NE
City Seattle
State/province WA
ZIP/Postal code 98195
Country USA
 
Platforms (2)
GPL13304 Illumina HiSeq 2000 (Drosophila melanogaster)
GPL19132 Illumina NextSeq 500 (Drosophila melanogaster)
Samples (4)
GSM2706365 Drosophila nuclei sci-ATAC-seq
GSM2860547 6-8hr WE Drosophila embryo nuclei DNAse-seq
GSM2860548 6-8hr elav+ Drosophila embryo nuclei DNAse-seq
Relations
BioProject PRJNA394875
SRA SRP112733

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE101581_RAW.tar 853.4 Mb (http)(custom) TAR (of BW, TXT)
Raw data are available in SRA
Processed data provided as supplementary file
Processed data is available on Series record

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